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RU2018138848A - NON-INVASIVE DIAGNOSIS BY SEQUENING 5-HYDROXYMETHYLEN CELLLESS DNA - Google Patents

NON-INVASIVE DIAGNOSIS BY SEQUENING 5-HYDROXYMETHYLEN CELLLESS DNA Download PDF

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RU2018138848A
RU2018138848A RU2018138848A RU2018138848A RU2018138848A RU 2018138848 A RU2018138848 A RU 2018138848A RU 2018138848 A RU2018138848 A RU 2018138848A RU 2018138848 A RU2018138848 A RU 2018138848A RU 2018138848 A RU2018138848 A RU 2018138848A
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bcdna
hydroxymethylation
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dna
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Стивен Р. КВЕЙК
Чуньсяо СУН
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Те Борд Оф Трастиз Оф Те Лилэнд Стэнфорд Джуниор Юниверсити
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Claims (42)

1. Способ секвенирования гидроксиметилированной бесклеточной ДНК (бкДНК), включающий:1. The method of sequencing hydroxymethylated cell-free DNA (bcDNA), including: (a) добавление адаптерных последовательностей на концы бкДНК;(a) adding adapter sequences to the ends of bcDNA; (b) инкубацию лигированной с адаптерами бкДНК с ДНК-β-глюкозилтрансферазой и UDP-глюкозой, модифицированной хемоселективной группой, при этом происходит ковалентное мечение молекул гидроксиметилированной ДНК в бкДНК хемоселективной группой;(b) incubation of the ligated with the bcDNA adapters with DNA-β-glucosyltransferase and UDP-glucose modified by the chemoselective group, with covalent labeling of the hydroxymethylated DNA molecules in the bcDNA with a chemoselective group; (c) присоединение биотинового компонента к хемоселективно модифицированной бкДНК по реакции циклоприсоединения;(c) attaching a biotin component to a chemoselectively modified bcDNA via a cycloaddition reaction; (d) обогащение биотинилированных молекул ДНК путем связывания продукта из стадии (c) с носителем, связывающимся с биотином;(d) enriching biotinylated DNA molecules by binding the product from step (c) to a carrier that binds to biotin; (e) амплификацию обогащенной ДНК с помощью праймеров, связывающихся с адаптерами; и(e) amplification of enriched DNA using primers that bind to adapters; and (f) секвенирование амплифицированной ДНК с получением множества прочтений последовательности,(f) sequencing the amplified DNA to obtain multiple readings of the sequence, причем способ не включает высвобождения биотинилированных молекул ДНК из носителя после стадии (d), перед стадией (e).moreover, the method does not include the release of biotinylated DNA molecules from the carrier after stage (d), before stage (e). 2. Способ анализа образцов, включающий:2. A method for analyzing samples, including: (a) идентификацию гидроксиметилированных последовательностей в образце бесклеточной ДНК (бкДНК) пациента путем:(a) the identification of hydroxymethylated sequences in a sample of cell-free DNA (bcDNA) of a patient by: (i) лигирования адаптерных последовательностей с бкДНК; (ii) модификации остатков гидроксиметилцитозина (5hmC) в бкДНК так, чтобы они содержали метку захвата; (iii) обогащения бкДНК, содержащей остатки гидроксиметилцитозина, путем связывания бкДНК с носителем через метку захвата, получая при этом обогащенную композицию, содержащую связанную с носителем гидроксиметилированную бкДНК; (iv) амплификации молекул бкДНК без высвобождения гидроксиметилированной бкДНК из носителя, получая амплифицированную ДНК; (v) секвенирования продуктов амплификации с получением множества прочтений последовательности; и (vi) идентификации гидроксиметилированных последовательностей в прочтениях последовательности;(i) ligation of adapter sequences with bcDNA; (ii) modifying the hydroxymethylcytosine residues (5hmC) in the bcDNA so that they contain a capture label; (iii) enriching the bcDNA containing hydroxymethylcytosine residues by binding the bcDNA to the carrier via a capture label, thereby obtaining an enriched composition comprising a hydroxymethylated bcDNA bound to the carrier; (iv) amplifying the bcDNA molecules without releasing the hydroxymethylated bcDNA from the carrier to produce amplified DNA; (v) sequencing amplification products to obtain multiple readings of the sequence; and (vi) identifying hydroxymethylated sequences in readings of the sequence; (b) сравнение идентифицированных гидроксиметилированных последовательностей с набором сигнатурных гидроксиметилированных последовательностей, коррелирующих с фенотипом; и (b) comparing the identified hydroxymethylated sequences with a set of signature hydroxymethylated sequences that correlate with the phenotype; and (c) составление отчета, показывающего корреляцию с фенотипом.(c) producing a report showing correlation with the phenotype. 3. Способ по п. 2, при этом захватная метка включает биотиновый компонент.3. The method according to claim 2, wherein the capture label includes a biotin component. 4. Способ по п. 3, при этом захватная метка вводится по остаткам гидроксиметилцитозина в бкДНК на стадии (a)(ii) способом, включающим: инкубацию лигированной с адаптерами бкДНК с ДНК-β-глюкозилтрансферазой и UDP-глюкозой, модифицированной хемоселективной группой, при этом хемоселективная группа ковалентно связывается с остатками 5hmC в бкДНК; и проведение реакции биотинового компонента с хемоселективной группой, получая биотинилированную, гидроксиметилированную бкДНК.4. The method according to claim 3, wherein the capture label is introduced at the residues of hydroxymethylcytosine into bcDNA in step (a) (ii) by a method comprising: incubating ligated with bcDNA adapters with DNA-β-glucosyl transferase and UDP-glucose modified by a chemoselective group, in this case, the chemoselective group covalently binds to 5hmC residues in bcDNA; and reacting the biotin component with a chemoselective group to produce biotinylated, hydroxymethylated bcDNA. 5. Способ по п. 4, при этом бкДНК подвергается амплификации на стадии (a)(iv) с помощью праймеров, связывающихся с адаптерами.5. The method of claim 4, wherein the bcDNA is amplified in step (a) (iv) using primers that bind to the adapters. 6. Способ по п. 5, дополнительно включающий, после стадии (a)(iii) и перед стадией (a)(iv), отмывку носителя и постановку реакции амплификации, содержащей носитель, без высвобождения биотинилированных молекул ДНК из носителя.6. The method of claim 5, further comprising, after step (a) (iii) and before step (a) (iv), washing the carrier and setting up an amplification reaction containing the carrier without releasing biotinylated DNA molecules from the carrier. 7. Способ по п. 4, при этом UDP-глюкоза, модифицированная хемоселективной группой, включает UDP-6-N3-Glu, биотиновый компонент включает биотин, модифицированный дибензоциклооктином, а носитель включает авидин или стрептавидин.7. The method according to claim 4, wherein the UDP glucose modified by the chemoselective group comprises UDP-6-N 3 -Glu, the biotin component comprises biotin modified with dibenzocyclooctin, and the carrier comprises avidin or streptavidin. 8. Способ по п. 2, при этом фенотипом является заболевание, состояние или клинический исход.8. The method of claim 2, wherein the phenotype is a disease, condition, or clinical outcome. 9. Способ по п. 2, при этом стадия (a)(vi) является количественной.9. The method according to claim 2, wherein step (a) (vi) is quantitative. 10. Способ по п. 9, при этом стадия (a) дополнительно включает определение уровня гидроксиметилирования у каждой идентифицированной гидроксиметилированной последовательности, получая первый профиль гидроксиметилирования, включающий уровень гидроксиметилирования у каждой идентифицированной последовательности.10. The method of claim 9, wherein step (a) further comprises determining a hydroxymethylation level for each identified hydroxymethylated sequence, obtaining a first hydroxymethylation profile including a hydroxymethylation level for each identified sequence. 11. Способ по п. 10, дополнительно включающий получение второго образца бкДНК от пациента в другой момент времени и повторение стадии (a) со вторым образцом, получая второй профиль гидроксиметилирования.11. The method of claim 10, further comprising obtaining a second bcDNA sample from the patient at another point in time and repeating step (a) with the second sample to obtain a second hydroxymethylation profile. 12. Способ по п. 11, дополнительно включающий сравнение второго профиля гидроксиметилирования с первым профилем гидроксиметилирования для выявления изменений в гидроксиметилировании с течением времени.12. The method of claim 11, further comprising comparing the second hydroxymethylation profile with the first hydroxymethylation profile to detect changes in hydroxymethylation over time. 13. Способ по п. 12, при этом сравнение приводит к получению карты изменений гидроксиметилирования в ходе заболевания или при лечении заболевания.13. The method according to p. 12, the comparison leads to a map of changes in hydroxymethylation during the disease or in the treatment of the disease. 14. Способ по п. 10, при этом набор сигнатурных последовательностей гидроксиметилирования включает карту целевых локусов в контрольном профиле гидроксиметилирования, а стадия (b) включает сравнение уровня гидроксиметилирования для каждой гидроксиметилированной последовательности с уровнем гидроксиметилирования в соответствующем целевом локусе.14. The method according to claim 10, wherein the set of signature hydroxymethylation sequences includes a map of target loci in the hydroxymethylation control profile, and step (b) includes comparing the hydroxymethylation level for each hydroxymethylation sequence with the hydroxymethylation level at the corresponding target locus. 15. Способ по п. 14, дополнительно включающий определение того, является ли каждая идентифицированная гидроксиметилированная последовательность по уровню гидроксиметилирования чрезмерно представленной или недостаточно представленной относительно уровня гидроксиметилирования в соответствующем целевом локусе.15. The method of claim 14, further comprising determining whether each identified hydroxymethylated sequence by the level of hydroxymethylation is overrepresented or underrepresented relative to the level of hydroxymethylation at the corresponding target locus. 16. Способ по п. 15, при этом способ дополнительно включает (e) получение диагноза, решения о лечении или прогноза, исходя из результатов по идентичности тех гидроксиметилированных последовательностей, которые чрезмерно или недостаточно представлены относительно соответствующих целевых локусов.16. The method according to claim 15, wherein the method further comprises (e) obtaining a diagnosis, treatment decision or prognosis based on the results of the identity of those hydroxymethylated sequences that are overly or underrepresented relative to the corresponding target loci. 17. Способ по п. 16, при этом диагноз, решение о лечении или прогноз составляет диагностику рака.17. The method of claim 16, wherein the diagnosis, treatment decision or prognosis is cancer diagnosis. 18. Способ по п. 17, при этом целевые локусы включают в себя одно или несколько тел следующих генов: ABRACL, ADAMTS4, AGFG2, ALDH1A3, ALG10B, AMOTL1, APCDD1L-AS1, ARL6IP6, ASF1B, ATP6V0A2, AUNIP, BAGE, C2orf62, C8orf22, CALCB, CC2D1B, CCDC33, CCNL2, CLDN15, COMMD6, CPLX2, CRP, CTRC, DACH1, DAZL, DDX11L1, DHRS3, DUSP26, DUSP28, EPN3, EPPIN-WFDC6, ETAA1, FAM96A, FENDRR, FLJ16779, FLJ31813, GBX1, GLP2R, GMCL1P1, GNPDA2, GPR26, GSTP1, HMOX2, HOXC5, IGSF9B, INSC, INSL4, IRF7, KIF16B, KIF20B, LARS, LDHD, LHX5, LINC00158, LINC00304, LOC100128946, LOC100131234, LOC100132287, LOC100506963, LOC100507250, LOC100507410, LOC255411, LOC729737, MAFF, NPAS4, NRADDP, P2RX2, PAIP1, PAX1, PODXL2, POU4F3, PSMG1, PTPN2, RAG1, RBM14-RBM4, RDH11, RFPL3, RNF122, RNF223, RNF34, SAMD11, SHISA2, SIGLEC10, SLAMF7, SLC25A46, SLC25A47, SLC9A3R2, SORD, SOX18, SPATA31E1, SSR2, STXBP3, SYT11, SYT2, TCEA3, THAP7-AS1, TMEM168, TMEM65, TMX2, TPM4, TPO, TRAM1, TTC24, UBQLN4, WASH7P, ZNF284, ZNF423, ZNF444, ZNF800, ZNF850 и ZRANB2.18. The method of claim 17, wherein the target loci include one or more bodies of the following genes: ABRACL, ADAMTS4, AGFG2, ALDH1A3, ALG10B, AMOTL1, APCDD1L-AS1, ARL6IP6, ASF1B, ATP6V0A2, AUNIP, BAGE, C2orf62 C8orf22, CALCB, CC2D1B, CCDC33, CCNL2, CLDN15, COMMD6, CPLX2, CRP, CTRC, DACH1, DAZL, DDX11L1, DHRS3, DUSP26, DUSP28, EPN3, EPPIN-WFDC6, ETAA1, FJ9, FJ9, GB16, GB18 GLP2R, GMCL1P1, GNPDA2, GPR26, GSTP1, HMOX2, HOXC5, IGSF9B, INSC, INSL4, IRF7, KIF16B, KIF20B, LARS, LDHD, LHX5, LINC00158, LINC00304, LOC1001212946, LOC100100 LOC5050669 LOC100502OCLOC50501, LOC1501502, LOC1505, LOC1505, LOC1505, LOC1505, LOC1505, LOC1505, LOC1505, LOC1505, LOC1505, LOC1502, LOC729737, MAFF, NPAS4, NRADDP, P2RX2, PAIP1, PAX1, PODXL2, POU4F3, PSMG1, PTPN2, RAG1, RBM14-RBM4, RDH11, RFPL3, RNF122, RNF223, RNF34, SAMDIGA2525, SAMDIGL2525, SAMD11L2525, SLCA, SLCA, SLCA SLC9A3R2, SORD, SOX18, SPATA31E1, SSR2, STXBP3, SYT11, SYT2, TCEA3, THAP7-AS1, TMEM168, TMEM65, TMX2, TPM4, TPO, TRAM1, TTC24, UBQLN4, WASH7P, ZNF284, ZNF423, ZNF444, ZNF800, ZNF850 and ZRANB2. 19. Способ по п. 18, при этом адаптерные последовательности содержат молекулярный баркод.19. The method of claim 18, wherein the adapter sequences comprise a molecular barcode. 20. Способ по п. 19, при этом молекулярный баркод включает последовательность идентификатора образца и последовательность идентификатора молекулы.20. The method of claim 19, wherein the molecular barcode comprises a sequence of a sample identifier and a sequence of a molecule identifier. 21. Способ по п. 2, при этом перед стадией (a) в образец вносится композиция добавляемого контроля.21. The method according to claim 2, wherein, before step (a), the composition of the added control is introduced into the sample. 22. Способ по п. 21, при этом композиция добавляемого контроля включает три ампликона, синтезированных с помощью коктейля из dATP, dGTP, dTTP и (1) dCTP, (2) dmCTP или (3) dhmCTP и dCTP.22. The method of claim 21, wherein the added control composition comprises three amplicons synthesized using a cocktail of dATP, dGTP, dTTP and (1) dCTP, (2) dmCTP or (3) dhmCTP and dCTP. 23. Набор для анализа бкДНК, включающий:23. A kit for analysis of bcDNA, including: ДНК-β-глюкозилтрансферазу;DNA β-glucosyl transferase; UDP-глюкозу, модифицированную хемоселективной группой;UDP glucose modified by a chemoselective group; адаптер, содержащий по меньшей мере один молекулярный баркод; и an adapter containing at least one molecular barcode; and добавляемый контроль, включающий три ампликона, синтезированных с помощью коктейля из dATP, dGTP, dTTP и (1) dCTP, (2) dmCTP или (3) dhmCTP и dCTP.an added control comprising three amplicons synthesized using a cocktail of dATP, dGTP, dTTP and (1) dCTP, (2) dmCTP or (3) dhmCTP and dCTP. 24. Набор по п. 23, при этом по меньшей мере один баркод включает последовательность идентификатора образца и последовательность идентификатора молекулы.24. The kit of claim 23, wherein the at least one barcode comprises a sequence of a sample identifier and a sequence of a molecule identifier. 25. Образец, включающий:25. Sample including: пул молекул бесклеточной ДНК, лигированной с адаптерами, которые получены из нескольких разных источников и содержат один или несколько модифицированных гидроксиметилцитозинов, содержащих метку захвата, причем молекулы ДНК дополнительно включают в себя молекулярные баркоды, указывающие на их источники и позволяющие отличить последовательности из разных источников после анализа; и a pool of acellular DNA molecules ligated with adapters that are obtained from several different sources and contain one or more modified hydroxymethylcytosines containing a capture label, and the DNA molecules additionally include molecular barcodes indicating their sources and allowing to distinguish sequences from different sources after analysis ; and добавленный контроль, включающий три ампликона, синтезированных с помощью коктейля из dATP, dGTP, dTTP и (1) dCTP, (2) dmCTP или (3) dhmCTP и dCTP.added control, including three amplicons synthesized using a cocktail of dATP, dGTP, dTTP and (1) dCTP, (2) dmCTP or (3) dhmCTP and dCTP.
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